added github release download for parenchyma model

livermask/utils/fetch.py

@@ -0,0 +1,29 @@
+import os
+import requests
+from datetime import datetime
+from email.utils import parsedate_to_datetime, formatdate
+
+
+# taken from: https://lenon.dev/blog/downloading-and-caching-large-files-using-python/
+def download(url, destination_file):
+    headers = {}
+
+    if os.path.exists(destination_file):
+        mtime = os.path.getmtime(destination_file)
+        headers["if-modified-since"] = formatdate(mtime, usegmt=True)
+
+    response = requests.get(url, headers=headers, stream=True)
+    response.raise_for_status()
+
+    if response.status_code == requests.codes.not_modified:
+        return
+
+    if response.status_code == requests.codes.ok:
+        with open(destination_file, "wb") as f:
+            for chunk in response.iter_content(chunk_size=1048576):
+                f.write(chunk)
+        
+        last_modified = response.headers.get("last-modified")
+        if last_modified:
+            new_mtime = parsedate_to_datetime(last_modified).timestamp()
+            os.utime(destination_file, times=(datetime.now().timestamp(), new_mtime))

livermask/utils/utils.py

@@ -2,11 +2,12 @@ import gdown
 import logging as log
 import chainer
 from .unet3d import UNet3D
+from .fetch import download
 
 
 def get_model(output):
-    url = "https://drive.google.com/uc?id=12or5Q79at2BtLgQ7IaglNGPFGRlEgEHc"
-    gdown.cached_download(url, output)
+    url = "https://github.com/andreped/livermask/releases/download/trained-models-v1/model.h5"
+    download(url, output)
 
 
 def get_vessel_model(output):